Cowell was arrested on sodomy charges in 1936 after a 17 year old boy claimed to be his special friend. With the expectation to receive a light sentence and psychiatry, Cowell pleaded guilty to oral copulation with the minor, but the moral climate plus adverse newspaper publicity (dubbing him "California's Oscar Wilde) at the time forced the judge to issue a fifteen year sentence. After his release in 1940, he worked for the government and subsequently was granted a full pardon. In 1943 he became a music editor with the Office of War Information.